A poor start for the Catalans saw them fall two goals behind early on, before Adriano was shown a straight red card to leave them on the brink of defeat after only half an hour.
However, Lionel Messi reduced the arrears with a free kick on the stroke of half-time, and Barca recovered to give Madrid a run for their money during the second half, an improvement that was not lost on their coach.
"The first half was not like us, but the second half was one of my proudest nights with the team," Vilanova told reporters after the match.
"With 10 men we controlled the game and had five clear chances. We never sit back, defend with 10 and try to hit on the counter. With our players, we always play the same way and did so in the second half."
Vilanova also offered his compliments to Madrid for their victory, saying: "I would like to congratulate Madrid on winning the [Supercopa] title."
In the 221st meeting between the two sides, Los Blancos' triumph sees them move ahead of Barcelona 88-87 in the all-time ranking for Clasico victories.